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<table width="100%"><tr><td align="left"><a href="../index.html"><img alt="<" border="0" src="../left.png">&nbsp;Master index</a></td>
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<h1>Index for CellSort 1.2</h1>

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<td valign=center><i>CellSort</i> is a <a href="http://www.mathworks.com">MATLAB</a> toolbox containing code that accompanies the manuscript, <i>Automated analysis of cellular signals from large-scale calcium imaging data</i> by Eran Mukamel, Axel Nimmerjahn and Mark Schnitzer, <a href="http://www.cell.com/neuron">NEURON</a> (2009).  Please address comments and questions to <a href="http://www.people.fas.harvard.edu/~emukamel/">Eran Mukamel</a> (<u>eran at post dot harvard dot edu</u>).
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<td><img src="images/Mukamel1a.jpg" align="left"></td>

<h2>Matlab files in this directory:</h2>
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<tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp; Step 1: <a href="CellsortPCA.html">CellsortPCA</a></td><td>[mixedsig, mixedfilters, CovEvals, covtrace, movm, movtm] = CellsortPCA(fn, flims, nPCs, dsamp, outputdir, badframes) </td></tr>

<tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp; Step 2a: <a href="CellsortChoosePCs.html">CellsortChoosePCs</a></td><td>[PCuse] = CellsortChoosePCs(fn, mixedfilters) </td></tr>

<tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp; Step 2b: <a href="CellsortPlotPCspectrum.html">CellsortPlotPCspectrum</a></td><td>CellsortPlotPCspectrum(fn, CovEvals, pcuse) </td></tr>

<tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp; Step 3a: <a href="CellsortICA.html">CellsortICA</a></td><td>[ica_sig, ica_filters, ica_A, numiter] = CellsortICA(mixedsig, mixedfilters, PCuse, mu, nIC, ica_A_guess, termtol, maxrounds) </td></tr>

<tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp; Step 3b: <a href="CellsortICAplot.html">CellsortICAplot</a></td><td>CellsortICAplot(mode, ica_filters, ica_sig, f0, tlims, dt, ratebin, plottype, ICuse, spt, spc) </td></tr>


<tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp; Step 4a: <a href="CellsortSegmentation.html">CellsortSegmentation</a></td><td>[ica_segments, segmentlabel, segcentroid] = CellsortSegmentation(ica_filters, smwidth, thresh, arealims, plotting) </td></tr>

<tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp; Step 4b:<a href="CellsortApplyFilter.html">CellsortApplyFilter</a></td><td>cell_sig = CellsortApplyFilter(fn, ica_segments, flims, movm, subtractmean) </td></tr>

<tr><td><img src="../matlabicon.gif" alt="" border="">&nbsp; Step 5:<a href="CellsortFindspikes.html">CellsortFindspikes</a></td><td>[spmat, spt, spc, zsig] = CellsortFindspikes(ica_sig, thresh, dt, deconvtau, normalization) </td></tr>
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